In this study, we aimed to investigate possible abnormality of bladder endothelial cells in interstitial cystitis patients by detecting morphological changes such as apoptosis in bladder endothelial cells. A bladder biopsy specimen was collected from interstitial cystitis patients immediately after hydrodistension therapy. The patients were classified into two groups on the basis of their predominant symptom, one group of patients with bladder pain and another group of patients with urinary urgency. Dissociated cells from the biopsy specimen were analyzed by flow cytometry after staining with Annexin V and an anti-CD105 antibody. Terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) and electron microscopy were performed to confirm morphologic changes indicative of apoptosis. The percentage of Annexin V binding, an early apoptosis marker, was significantly higher in bladder endothelial cells from interstitial cystitis patients with pain [median 24.7% (range 15.1-77.2), n = 20, P < 0.01) than that from interstitial cystitis patients with urinary urgency [9.3% (range 0.7-19.11) n = 17) or control patients [1.5% (range 0.8-9.1), n = 7]. TUNEL staining showed apoptotic cells in microvascular endothelial cells but not in the endothelial cells of a venule. By electron microscopy, endothelial cells showed morphological changes indicative of apoptosis such as nuclear fragmentation. Our results indicate that increased apoptosis of bladder microvascular endothelial cells may play an important role in the pathogenesis of interstitial cystitis accompanied by bladder pain.